BCFtools Allelic Depth format nowhere explained?

Question

[chrisgr]

Hi, I had a question about Allelic depth (AD) of BCFtools.

It has this format e.g. AD=262,18,0 - What number shows the depth of the REF and what is the ALT? and what is the '0'? I found 1 form where someone said 262 is the REF and 18 is the ALT. Is that correct?

I would also like to know why this format is explained nowhere in the manuals.. It seems to me like something everyone would be interested in.

Thank you in advance,

-Chris

[chrisgr]

I noticed that it follows the same format as the ref and alt collumn of the vcf so, 262 indecates the REF, the 18 the most occuring alt, and the 0 the depth of the 2nd most occuring alt

Answer 1

[Pierre Lindenbaum]

I'm sure AD is described in your VCF header.....

AD=262,18,0

is a tri-allelic variant. 262 reads are REF, 18 are ALT n°1, 0 are ALT n°2

[chrisgr]

Thanks for the reply!

But no, not in the VCF header. It says only this:

FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths">

INFO=<ID=AD,Number=R,Type=Integer,Description="Total allelic depths">

Thank you for the explanation!

-Chris

[Pierre Lindenbaum]

FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths"> . So all the information you need is here. See the VCF spec for the meaning of Number=R...

[chrisgr]

Oh I see!

Thank you!